# NM_025243.4(SLC19A3):c.12C>T (p.Tyr4=)

https://sugi.bio/variant/slc19a3-p-tyr4

## Summary

**SLC19A3 p.Tyr4= (c.12C>T)** is classified **Likely benign** in SLC19A3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-25). Very rare (popmax 0.0011%, sas); Associated with biotin-responsive basal ganglia disease.

**At a glance:** Likely benign · review: Single submitter · 1 submitter · 1 linked condition · very rare (popmax 0.0011%, sas)

## For patients & families {#patients}

This is a change in the SLC19A3 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to biotin-responsive basal ganglia disease.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | Adolescent |
| Clinical trials | 1 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | SLC19A3 is a diagnostic-grade gene on 16 Genomics England panels |

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0010237/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [SLC19A3](https://sugi.bio/atlas/gene/SLC19A3/) |
| Protein change (HGVS p.) | p.Tyr4= |
| Coding change (HGVS c.) | c.12C>T |
| MANE Select transcript | [NM_025243](https://www.ncbi.nlm.nih.gov/nuccore/NM_025243) |
| Variant type | single nucleotide variant |
| Location | chr2:227702307-227702307 (GRCh38) |
| ClinVar | [VCV3665036](https://www.ncbi.nlm.nih.gov/clinvar/variation/3665036/) |

**All HGVS expressions:** `NC_000002.11:g.228567023G>A`, `NC_000002.12:g.227702307G>A`, `NG_016359.1:g.20723C>T`, `NM_001371411.1:c.12C>T`, `NM_001371412.1:c.12C>T`, `NM_001371413.1:c.-197C>T`, `NM_001371414.1:c.-197C>T`, `NM_025243.4:c.12C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation and, for splice-region changes, SpliceAI (below), not from a missing predictor score.
- SpliceAI predicts **acceptor loss** (Δ 0.22) — a splice-altering prediction the current classification does not reflect
- Conservation: phyloP 1.822, GERP -2.86, phastCons 0.903 — weakly conserved position
- CADD: **PHRED 0.16**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI deltas (raw): acceptor loss **0.22**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**. Largest is acceptor loss.
- SpliceAI deltas (masked): acceptor loss **0.22**, donor loss **0.00**, acceptor gain **0.00**, donor gain **0.00**.
- Population frequency (gnomAD v4.1): grpmax **0.0011%** (sas) · FAF95 7.9e-05% · FAF99 5.4e-05% · 1/91,074 in the highest group · 6/1,613,916 alleles overall — very rare (popmax 0.0011%, sas).

| Ancestry group | Allele frequency | 1 in |
| --- | --- | --- |
| Remaining individuals (not grpmax-eligible) | 0.0016% | 62,504 |
| South Asian (grpmax) | 0.0011% | 91,074 |
| European (non-Finnish) | 0.000339% | 294,989 |

Remaining individuals shows a higher raw frequency than the grpmax group. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and "Remaining individuals" — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**SLC19A3** population constraint: LOEUF 0.968, pLI 1.2033e-07, missense-Z 0.51867. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **Leigh syndrome** — Definitive (AR)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 81.96, 55% of residues very-high.

**19 experimental structure(s)** (PDB): [8S4U](https://www.rcsb.org/structure/8S4U), [8S5U](https://www.rcsb.org/structure/8S5U), [8S5W](https://www.rcsb.org/structure/8S5W), [8S5Z](https://www.rcsb.org/structure/8S5Z), [8S61](https://www.rcsb.org/structure/8S61), [8S62](https://www.rcsb.org/structure/8S62).

## What this gene does {#gene-function}

*Describes the biological roles of SLC19A3 (the gene this variant disrupts) — not effects measured for this specific variant. A damaging variant is expected to affect these functions and pathways; the degree depends on the variant.*


### Pathways affected {#pathways}

SLC19A3 participates in **1 Reactome pathway** (⚕ = disease pathway):

| Pathway (Reactome) | Evidence |
| --- | --- |
| [Vitamin B1 (thiamin) metabolism](https://reactome.org/content/detail/R-HSA-196819) | curated |

### Molecular function & processes (GO — experimentally supported) {#go}

**Biological process:** thiamine transport, pyridoxine transport.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2024-04-25.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2024-04-25 |

## Associated conditions {#conditions}

[biotin-responsive basal ganglia disease](https://sugi.bio/atlas/disease/biotin-responsive-basal-ganglia-disease/).

**Reported phenotype names (ClinVar):** Biotin-responsive basal ganglia disease, Thiamine Transporter-2 Deficiency, THIAMINE METABOLISM DYSFUNCTION SYNDROME 2 (BIOTIN- AND THIAMINE-RESPONSIVE TYPE), Thiamine metabolism dysfunction syndrome type 2, Thiamine metabolism dysfunction syndrome 2 (biotin- or thiamine-responsive encephalopathy type 2), thiamine-responsive encephalopathy.

## Same-residue context {#hotspot}

Residue **4** carries **1 other pathogenic ClinVar variant** — a recurrently-mutated position: [SLC19A3 p.Tyr4Ter](/variant/slc19a3-p-tyr4ter). *Positional co-occurrence of independent ClinVar records, not functional proof.*

## Similar variants {#similar}

Related SLC19A3 variant pages (same residue, condition, or type): [SLC19A3 p.Tyr4Ter](/variant/slc19a3-p-tyr4ter), [SLC19A3 p.Tyr4Asn](/variant/slc19a3-p-tyr4asn), [SLC19A3 c.1172+1G>A](/variant/slc19a3-c-1172-plus-1g-a), [SLC19A3 c.1172+2T>G](/variant/slc19a3-c-1172-plus-2t-g), [SLC19A3 c.1173-1G>A](/variant/slc19a3-c-1173-minus-1g-a), [SLC19A3 c.151-1G>C](/variant/slc19a3-c-151-minus-1g-c), [SLC19A3 c.980-14A>G](/variant/slc19a3-c-980-minus-14a-g), [SLC19A3 p.Gly23Val](/variant/slc19a3-p-gly23val).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-14); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 3665036). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*